1. 3B1
Gene regulation results in differential GENE EXPRESSION, LEADING TO CELL SPECIALIZATION

2. Control of Gene Expression
Controlling gene expression is often accomplished by controlling transcription initiation
Regulatory proteins bind to DNA
May block or stimulate transcription
Prokaryotic organisms regulate gene expression in response to their environment
Eukaryotic cells regulate gene expression to maintain homeostasis in the organism

3. Regulatory Proteins
Gene expression is often controlled by regulatory proteins binding to specific DNA sequences
Regulatory proteins gain access to the bases of DNA at the major groove
Regulatory proteins possess DNA-binding motifs

4. Prokaryotic regulation
Control of transcription initiation
Positive control – increases frequency of initiation of transcription
Activators enhance binding of RNA polymerase to promoter
Effector molecules can enhance or decrease
Negative control – decreases frequency
Repressors bind to operators in DNA
Allosterically regulated
Respond to effector molecules – enhance or abolish binding to DNA

5. Prokaryotic cells often respond to their environment by changes in gene expression
Genes involved in the same metabolic pathway are organized in operons
Induction – enzymes for a certain pathway are produced in response to a substrate
Repression – capable of making an enzyme but does not

6. Eukaryotic Regulation
Control of transcription more complex
Major differences from prokaryotes
Eukaryotes have DNA organized into chromatin
Complicates protein-DNA interaction
Eukaryotic transcription occurs in nucleus
Amount of DNA involved in regulating eukaryotic genes much larger

7. Transcription factors
General transcription factors
Necessary for the assembly of a transcription apparatus and recruitment of RNA polymerase II to a promoter
TFIID recognizes TATA box sequences
Specific transcription factors
Increase the level of transcription in certain cell types or in response to signals

8. Before the start of transcription, the transcription Factor II D (TFIID) complex binds to the TATA box in the core promoter of the gene.
The TATA box (also called Goldberg-Hogness box)[1] is a DNA sequence (cis-regulatory element) found in the promoter region of genes in archaea and eukaryotes;[2] approximately 24% of human genes contain a TATA box within the core promoter.[3]
Considered to be the core promoter sequence, it is the binding site of either general transcription factors or histones (the binding of a transcription factor blocks the binding of a histone and vice versa) and is involved in the process of transcription by RNA polymerase.

10. Mediate the binding of RNA polymerase II to the promoter
Promoters form the binding sites for general transcription factors
Mediate the binding of RNA polymerase II to the promoter
Enhancers are the binding site of the specific transcription factors
DNA bends to form loop to position enhancer closer to promoter

12. Mediators essential to some but not all transcription factors
Coactivators and mediators are also required for the function of transcription factors
Bind to transcription factors and bind to other parts of the transcription apparatus
Mediators essential to some but not all transcription factors
Number of coactivators is small because used with multiple transcription factors

13. Transcription complex
Few general principles
Nearly every eukaryotic gene represents a unique case
Great flexibility to respond to many signals
Virtually all genes that are transcribed by RNA polymerase II need the same suite of general factors to assemble an initiation complex

15. Eukaryotic chromatin structure
Structure is directly related to the control of gene expression
DNA wound around histone proteins to form nucleosomes
Nucleosomes may block access to promoter
Histones can be modified to result in greater condensation

16. Methylation once thought to play a major role in gene regulation
Many inactive mammalian genes are methylated
Lesser role in blocking accidental transcription of genes turned off
Histones can be modified
Correlated with active versus inactive regions of chromatin
Can be methylated – found in inactive regions
Can be acetylated – found in active regions

17. Some coactivators have been shown to be histone acetylases
Transcription is increased by removing higher order chromatin structure that would prevent transcription
“Histone code” postulated to underlie the control of chromatin structure

18. Chromatin-remodeling complexes
Large complex of proteins
Modify histones and DNA
Also change chromatin structure
ATP-dependent chromatin remodeling factors
Function as molecular motors
Catalyze 4 different changes in DNA/histone binding
Make DNA more accessible to regulatory proteins

19. Pi ATP ADP + ATP -dependent remodeling factor 1. Nucleosome sliding
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
ATP
ADP + Pi
ATP -dependent
remodeling factor
1. Nucleosome sliding
2. Remodeled nucleosome
3. Nucleosome displacement
4. Histone replacement

20. Posttranscriptional Regulation
Control of gene expression usually involves the control of transcription initiation
Gene expression can be controlled after transcription with
Small RNAs
miRNA and siRNA
Alternative splicing
RNA editing
mRNA degradation

21. Micro RNA or miRNA
Production of a functional miRNA begins in the nucleus
Ends in the cytoplasm with a ~22 nt RNA that functions to repress gene expression
miRNA loaded into RNA induced silencing complex (RISC)
RISC is targeted to repress the expression of genes based on sequence complementarity to the miRNA

22. Copyright © The McGraw-Hill Companies, Inc
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
RNA Polymerase II
RNA Polymerase II
microRNA gene
microRNA gene
Pri-microRNA
Pri-microRNA
Nucleus
Nucleus
Drosha
Pre-microRNA
Pre-microRNA
Drosha
Exportin 5
Exportin 5
Cytoplasm
Dicer
Mature miRNA
RISC
mRNA
RISC
mRNA cleavage
mRNA
RISC
RISC 22
Inhibition of translation

23. Protein Degradation
Proteins are produced and degraded continually in the cell
Lysosomes house proteases for nonspecific protein digestion
Proteins marked specifically for destruction with ubiquitin
Degradation of proteins marked with ubiquitin occurs at the proteasome